rs348644

Variant names:

• chr12-62069922-A-C
• rs348644
• NM_178539.5:c.-2+121337T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178539.5(TAFA2):​c.-2+121337T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,038 control chromosomes in the GnomAD database, including 35,421 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (35421 hom., cov: 32)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 4 publications found

Genes affected

TAFA2 (HGNC:21589): (TAFA chemokine like family member 2) This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that act as regulators of immune and nervous cells. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.-2+121337T>G		intron_variant	Intron 1 of 4	ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.-2+121337T>G		intron_variant	Intron 1 of 4	1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103176 AN: 151920 Hom.: 35364 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.662

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.679 AC: 103298 AN: 152038 Hom.: 35421 Cov.: 32 AF XY: 0.682 AC XY: 50669 AN XY: 74338

African (AFR) AF: 0.746 AC: 30951 AN: 41474

American (AMR) AF: 0.703 AC: 10731 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3576 AN: 5172

South Asian (SAS) AF: 0.638 AC: 3073 AN: 4820

European-Finnish (FIN) AF: 0.709 AC: 7498 AN: 10574

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43350 AN: 67944

Other (OTH) AF: 0.669 AC: 1412 AN: 2112

Alfa AF: 0.641 Hom.: 28513

Bravo AF: 0.681

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.75
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs348644; hg19: chr12-62463703;